title: Implementation of a custom hardware-accelerator for short-read mapping using Burrows-Wheeler alignment.
abstract: The mapping of millions of short DNA fragments to a large genome is a great challenge in modern computational biology. Usually, it takes many hours or days to map a large genome using software. However, the recent progress of programmable hardware such as field programmable gate arrays (FPGAs) provides a cost effective solution to this challenge. FPGAs contain millions of programmable logic gates to design massively parallel accelerators. This paper proposes a hardware architecture to accelerate the short-read mapping using Burrows-Wheeler alignment. The speed-up of the proposed architecture is estimated to be at least 10 times compared to its equivalent software application.
authors.forename: Hasitha Muthumala
authors.initials: HM
authors.lastname: Waidyasooriya
authors.forename: Masanori
authors.initials: M
authors.lastname: Hariyama
authors.forename: Michitaka
authors.initials: M
authors.lastname: Kameyama
mesh_terms: D001483:Base Sequence; D003201:Computers; D001330:Electronic Data Processing; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software